Dear John,
Many thanks for the references. Much obliged.
With regard to question 2, probably I wasn't clear enough. I should have asked "how accurate are the MMPB(GB)SA methods in calculating ΔGs from a few snapshots only. Is there a threshold below which the results obtained are meaningless".
Best regards
George
On Mar 5, 2012, at 2:37 PM, Cannon, John F. wrote:
> Dear George,
>
> Question 1: Here are two references that might be useful to get started.
>
> Hou T, Wang J, Li Y, Wang W. 2011 Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model. Jan 24;51(1):69-82. http://pubs.acs.org/doi/full/10.1021/ci100275a
>
> Singh N, Warshel A. 2010 Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Proteins. 78(7):1705-23. http://www.ncbi.nlm.nih.gov/pubmed/20186976
>
> Question 2: The clustering is probably based on interatomic distances and therefore configuration, not on energy. If you have 100-1000's of trajectory snapshots, why would you not want an average to make sure you did not choose an outlier?
>
> John Cannon
> Genetics Program Chair and
> Associate Professor of
> Molecular Microbiology and Immunology
> University of Missouri
> 1 Hospital Drive
> Columbia, Missouri 65212
>
>
> -----Original Message-----
> From: George Tzotzos [mailto:gtzotzos.me.com]
> Sent: Saturday, March 03, 2012 7:05 AM
> To: AMBER Mailing List
> Subject: [AMBER] MMPB(GB)SA: two questions
>
> Hi everybody,
>
> I'd like to ask if any can shed light on the following:
>
> 1. Is there any study comparing ΔGs obtained form MMPBSA and MMGBSA to experimental values?
>
> 2. Are ΔGs obtained from one or very few trajectory snapshot reliable? This because clustering analysis produces on occasions clusters with 1 or very few members.
>
> Thanks in advance for any suggestions
>
> Regards
>
> George
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 05 2012 - 09:30:03 PST
